Objective: The objective of this study was to analyze the influence of maternal demographic characteristics and abnormal first-trimester sonographic markers on congenital anomalies (CAs) at birth when the fetus is structurally normal at the 11- to 14-week ultrasound.Methods: This prospective cohort study comprised high-risk women undergoing routine antenatal care. Detailed assessments of fetal anatomy and first-trimester sonographic markers were performed at 11-14 weeks of pregnancy. Multilevel regression analysis was used to determine the effects of maternal characteristics and abnormal first-trimester sonographic markers on the incidence of CA at birth.Results: Three hundred and ten patients were evaluated, and 41 patients (13.2%) had an anomalous newborn. The presence of a specific indication at the first-trimester ultrasound (OR: 2.72; CI 95% 1.09-6.74) or a nuchal translucency (NT) thickness greater than 2.5 mm increased the risk of CA at birth by three fold (OR: 3.10; CI 95% 1.07-9.59). High adjusted risks for trisomies 21, 18 and 13 increased the likelihood of having a structurally abnormal newborn by five, twelve and six fold, respectively.Conclusion: Increased NT and/or high adjusted risks for trisomies 21, 18, and 13 increase the risk of CA at birth, even in fetuses with a structurally normal 11- to 14-week ultrasound scan.